Zinc in PDB 7vb5: Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin

Enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin

All present enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin:
4.1.2.46;

Protein crystallography data

The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin, PDB code: 7vb5 was solved by D.Zheng, M.Nakabayashi, Y.Asano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.98 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.12, 51.57, 170, 90, 94.67, 90
R / Rfree (%) 17.1 / 20.5

Other elements in 7vb5:

The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin (pdb code 7vb5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin, PDB code: 7vb5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7vb5

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Zinc binding site 1 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:17.5
occ:1.00
 SG A:CYS121 2.2 18.7 1.0
SG A:CYS115 2.3 17.6 1.0
SG A:CYS129 2.4 16.8 1.0
SG A:CYS118 2.4 16.5 1.0
CB A:CYS121 3.3 17.9 1.0
CB A:CYS129 3.4 15.6 1.0
CB A:CYS115 3.4 18.3 1.0
CB A:CYS118 3.4 17.3 1.0
N A:CYS115 3.5 17.0 1.0
CA A:CYS129 3.7 15.3 1.0
N A:CYS118 3.9 19.5 1.0
N A:GLN116 3.9 21.0 1.0
CA A:CYS115 3.9 17.3 1.0
N A:GLN130 4.0 15.8 1.0
CA A:CYS118 4.2 18.0 1.0
N A:CYS121 4.2 17.1 1.0
C A:CYS129 4.3 15.9 1.0
C A:CYS115 4.3 21.2 1.0
CA A:CYS121 4.3 17.3 1.0
N A:ASN131 4.5 17.2 1.0
N A:THR117 4.5 22.9 1.0
C A:GLU114 4.6 16.4 1.0
O A:HOH862 4.7 23.5 1.0
OD1 A:ASN131 4.7 24.0 1.0
CA A:GLN116 4.9 23.2 1.0
CB A:ASN131 4.9 19.7 1.0
C A:CYS118 4.9 16.1 1.0
O A:CYS118 4.9 16.6 1.0
CA A:GLU114 4.9 17.3 1.0

Zinc binding site 2 out of 8 in 7vb5

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Zinc binding site 2 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:14.9
occ:1.00
 NE2 A:HIS85 2.0 13.0 1.0
SG A:CYS63 2.3 13.9 1.0
SG A:CYS199 2.3 14.6 1.0
N5 A:CNH504 2.5 17.2 1.0
CE1 A:HIS85 3.0 13.6 1.0
CD2 A:HIS85 3.1 14.0 1.0
CB A:CYS63 3.2 13.2 1.0
C5N A:NAD501 3.4 12.4 1.0
C4 A:CNH504 3.4 28.0 1.0
CB A:CYS199 3.5 15.3 1.0
C4N A:NAD501 3.6 12.7 1.0
C6N A:NAD501 3.9 12.3 1.0
ND1 A:HIS85 4.1 12.9 1.0
CG A:HIS85 4.2 13.0 1.0
CB A:THR65 4.2 11.9 1.0
O A:HOH772 4.4 14.6 1.0
C3N A:NAD501 4.4 11.7 1.0
OE2 A:GLU86 4.5 18.2 1.0
OG1 A:THR65 4.5 13.2 1.0
CA A:CYS63 4.6 12.9 1.0
N1N A:NAD501 4.7 12.2 1.0
C1 A:CNH504 4.8 31.8 1.0
O A:HOH672 4.8 15.7 1.0
CA A:CYS199 4.8 14.2 1.0
C2N A:NAD501 4.9 12.1 1.0
C2 A:CNH504 4.9 30.8 1.0
CG2 A:THR65 4.9 13.0 1.0

Zinc binding site 3 out of 8 in 7vb5

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Zinc binding site 3 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:16.8
occ:1.00
 SG B:CYS121 2.3 17.4 1.0
SG B:CYS129 2.3 17.2 1.0
SG B:CYS118 2.4 16.7 1.0
SG B:CYS115 2.4 18.4 1.0
CB B:CYS129 3.4 16.6 1.0
CB B:CYS121 3.4 18.2 1.0
CB B:CYS118 3.5 17.5 1.0
CB B:CYS115 3.5 17.8 1.0
N B:CYS115 3.5 17.9 1.0
CA B:CYS129 3.7 15.2 1.0
CA B:CYS115 3.9 18.6 1.0
N B:CYS118 3.9 18.5 1.0
N B:GLN116 3.9 21.8 1.0
N B:GLN130 3.9 13.9 1.0
N B:CYS121 4.2 16.1 1.0
CA B:CYS118 4.2 17.3 1.0
C B:CYS129 4.2 15.1 1.0
C B:CYS115 4.3 21.0 1.0
CA B:CYS121 4.3 17.2 1.0
N B:ASN131 4.5 16.1 1.0
N B:THR117 4.5 22.1 1.0
C B:GLU114 4.5 17.2 1.0
OD1 B:ASN131 4.6 24.9 1.0
O B:HOH867 4.7 21.9 1.0
CB B:ASN131 4.8 19.8 1.0
C B:CYS118 4.9 16.5 1.0
O B:CYS118 4.9 15.4 1.0
CA B:GLN116 4.9 22.4 1.0
CA B:GLU114 4.9 16.3 1.0

Zinc binding site 4 out of 8 in 7vb5

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Zinc binding site 4 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:15.1
occ:1.00
 NE2 B:HIS85 2.0 12.9 1.0
SG B:CYS63 2.3 13.7 1.0
SG B:CYS199 2.3 13.3 1.0
N5 B:CNH504 2.3 17.3 1.0
CE1 B:HIS85 3.0 13.0 1.0
CD2 B:HIS85 3.1 11.6 1.0
CB B:CYS63 3.2 14.1 1.0
C5N B:NAD501 3.4 12.1 1.0
C4 B:CNH504 3.4 23.4 1.0
CB B:CYS199 3.5 12.6 1.0
C4N B:NAD501 3.6 12.9 1.0
C6N B:NAD501 4.0 12.5 1.0
ND1 B:HIS85 4.1 12.7 1.0
CG B:HIS85 4.2 12.1 1.0
CB B:THR65 4.3 12.7 1.0
OE2 B:GLU86 4.3 17.3 1.0
O B:HOH789 4.4 14.4 1.0
C3N B:NAD501 4.4 11.4 1.0
OG1 B:THR65 4.4 13.7 1.0
CA B:CYS63 4.6 13.1 1.0
O B:HOH705 4.7 12.6 1.0
N1N B:NAD501 4.7 11.4 1.0
CA B:CYS199 4.8 12.6 1.0
C1 B:CNH504 4.8 28.4 1.0
C2N B:NAD501 4.9 11.0 1.0

Zinc binding site 5 out of 8 in 7vb5

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Zinc binding site 5 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:24.6
occ:1.00
 SG C:CYS129 2.3 22.9 1.0
SG C:CYS115 2.3 28.2 1.0
SG C:CYS121 2.3 23.8 1.0
SG C:CYS118 2.4 23.4 1.0
CB C:CYS121 3.4 24.4 1.0
CB C:CYS118 3.4 27.1 1.0
CB C:CYS129 3.4 23.0 1.0
CB C:CYS115 3.5 28.2 1.0
N C:CYS115 3.6 28.9 1.0
CA C:CYS129 3.7 19.9 1.0
N C:GLN116 3.9 27.8 1.0
N C:CYS118 4.0 25.9 1.0
N C:GLN130 4.0 20.5 1.0
CA C:CYS115 4.0 30.0 1.0
N C:CYS121 4.2 23.5 1.0
CA C:CYS118 4.2 27.1 1.0
C C:CYS129 4.3 19.8 1.0
CA C:CYS121 4.3 22.5 1.0
C C:CYS115 4.3 30.2 1.0
N C:ASN131 4.5 25.1 1.0
N C:THR117 4.5 31.0 1.0
O C:HOH780 4.6 27.3 1.0
C C:GLU114 4.6 27.7 1.0
OD1 C:ASN131 4.7 32.4 1.0
O C:CYS118 4.8 24.9 1.0
C C:CYS118 4.8 26.1 1.0
CB C:ASN131 4.9 27.8 1.0
CA C:GLN116 4.9 30.8 1.0
CA C:GLU114 4.9 26.9 1.0

Zinc binding site 6 out of 8 in 7vb5

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Zinc binding site 6 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:23.3
occ:0.96
 NE2 C:HIS85 1.9 20.0 1.0
SG C:CYS63 2.2 22.6 1.0
SG C:CYS199 2.3 21.4 1.0
N5 C:CNH504 2.4 21.0 1.0
CE1 C:HIS85 2.8 20.9 1.0
CD2 C:HIS85 3.0 20.8 1.0
CB C:CYS63 3.2 24.1 1.0
C5N C:NAD501 3.3 19.7 1.0
C4 C:CNH504 3.4 34.4 1.0
CB C:CYS199 3.5 21.6 1.0
C4N C:NAD501 3.6 22.1 1.0
C6N C:NAD501 3.9 19.8 1.0
ND1 C:HIS85 4.0 20.4 1.0
CG C:HIS85 4.1 20.5 1.0
CB C:THR65 4.2 21.7 1.0
OE2 C:GLU86 4.4 25.7 1.0
O C:HOH709 4.4 22.2 1.0
C3N C:NAD501 4.4 21.5 1.0
OG1 C:THR65 4.6 21.4 1.0
CA C:CYS63 4.6 21.8 1.0
N1N C:NAD501 4.7 20.1 1.0
O C:HOH704 4.7 24.3 1.0
C1 C:CNH504 4.8 35.7 1.0
CA C:CYS199 4.8 20.9 1.0
C2N C:NAD501 4.9 19.5 1.0
CG2 C:THR65 4.9 22.7 1.0

Zinc binding site 7 out of 8 in 7vb5

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Zinc binding site 7 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:24.2
occ:0.86
 SG D:CYS121 2.2 29.1 1.0
SG D:CYS129 2.2 29.6 1.0
SG D:CYS118 2.4 29.6 1.0
SG D:CYS115 2.4 29.3 1.0
CB D:CYS129 3.4 25.4 1.0
CB D:CYS121 3.4 30.3 1.0
CB D:CYS115 3.5 32.0 1.0
CB D:CYS118 3.5 32.5 1.0
N D:CYS115 3.5 30.6 1.0
CA D:CYS129 3.7 22.9 1.0
N D:GLN130 3.9 25.2 1.0
N D:GLN116 3.9 32.3 1.0
CA D:CYS115 3.9 31.9 1.0
N D:CYS118 3.9 35.4 1.0
N D:CYS121 4.2 26.7 1.0
C D:CYS129 4.2 24.9 1.0
CA D:CYS118 4.2 30.6 1.0
C D:CYS115 4.3 33.3 1.0
CA D:CYS121 4.4 29.2 1.0
N D:ASN131 4.4 28.6 1.0
N D:THR117 4.5 32.0 1.0
C D:GLU114 4.6 27.4 1.0
OD1 D:ASN131 4.7 33.4 1.0
O D:HOH761 4.7 34.1 1.0
CB D:ASN131 4.8 32.7 1.0
C D:CYS118 4.9 28.9 1.0
CA D:GLU114 4.9 27.6 1.0
O D:CYS118 4.9 29.3 1.0
CA D:GLN116 4.9 31.9 1.0
CA D:GLN130 5.0 27.2 1.0
N D:CYS129 5.0 22.5 1.0

Zinc binding site 8 out of 8 in 7vb5

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Zinc binding site 8 out of 8 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum Complexed with Acetone Cyanohydrin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:23.1
occ:0.95
 NE2 D:HIS85 2.1 21.7 1.0
SG D:CYS199 2.2 22.1 1.0
SG D:CYS63 2.3 23.3 1.0
O D:HOH766 2.5 24.4 1.0
CD2 D:HIS85 3.0 20.5 1.0
CE1 D:HIS85 3.2 21.8 1.0
CB D:CYS63 3.2 23.4 1.0
C5N D:NAD501 3.4 23.4 1.0
CB D:CYS199 3.5 20.1 1.0
C4N D:NAD501 3.6 22.9 1.0
C6N D:NAD501 3.9 23.7 1.0
CG D:HIS85 4.2 21.1 1.0
CB D:THR65 4.2 23.9 1.0
ND1 D:HIS85 4.2 21.5 1.0
O D:HOH699 4.4 19.9 1.0
OG1 D:THR65 4.4 24.7 1.0
OE2 D:GLU86 4.4 25.3 1.0
C3N D:NAD501 4.5 23.7 1.0
CA D:CYS63 4.7 21.8 1.0
N1N D:NAD501 4.7 23.3 1.0
CA D:CYS199 4.8 20.2 1.0
O D:HOH656 4.8 22.8 1.0
C2 D:ACN506 4.9 41.3 1.0
C2N D:NAD501 4.9 22.8 1.0
CG2 D:THR65 5.0 24.4 1.0

Reference:

D.Zheng, M.Nakabayashi, Y.Asano. Structural Characterization of Linum Usitatissimum Hydroxynitrile Lyase: A New Cyanohydrin Decomposition Mechanism Involving A Cyano-Zinc Complex. J.Biol.Chem. V. 298 01650 2022.
ISSN: ESSN 1083-351X
PubMed: 35101448
DOI: 10.1016/J.JBC.2022.101650
Page generated: Wed Oct 30 12:37:18 2024

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